Hi Matt,
I think we'd prefer a Fortran wrapper for DMPlexGetGlobalOffset_Internal().
We've got our heads around offsets now and are happy working with them.
In a relate query, when we're setting up a new vector with a different dof then
we follow the approach you use in plexgeometry.c (see example code snippet
below). But I don't understand why when we run this in parallel we DON'T need
to check if the cell is off-process before calling PetscSectionSetDof. In fact
when I did check (using the ghost label approach) it then gave the error:
"Global dof 1 for point 1 is not the unconstrained 0" (see full error log
below)?
Thanks!
call DMPlexGetHeightStratum(dm, 0, start_cell, end_cell, ierr);
CHKERRQ(ierr)
call DMPlexGetHybridBounds(dm, end_interior_cell, &
PETSC_NULL_INTEGER, PETSC_NULL_INTEGER, PETSC_NULL_INTEGER, ierr);
CHKERRQ(ierr)
call DMClone(dm, dmRocks, ierr); CHKERRQ(ierr)
call PetscSectionCreate(PETSC_COMM_WORLD, rocks_section, ierr);
CHKERRQ(ierr)
call PetscSectionSetChart(rocks_section, start_cell, end_interior_cell,
ierr); CHKERRQ(ierr)
do c = start_cell, end_interior_cell-1
! Want a new vector with 4 dofs
! Doesn't work if we exclude cells that are off-process
call PetscSectionSetDof(rocks_section, c, 4, ierr); CHKERRQ(ierr)
end do
call PetscSectionSetUp(rocks_section, ierr); CHKERRQ(ierr)
call DMSetDefaultSection(dmRocks, rocks_section, ierr); CHKERRQ(ierr)
call DMCreateGlobalVector(dmRocks, rockproperties, ierr); CHKERRQ(ierr)
The full error log if we exclude off-process cells during PetscSectionSetDof:
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: Invalid argument
[0]PETSC ERROR: Global dof 1 for point 1 is not the unconstrained 0
[1]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[1]PETSC ERROR: Invalid argument
[1]PETSC ERROR: Global dof 1 for point 2 is not the unconstrained 0
[1]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for
trouble shooting.
[1]PETSC ERROR: Petsc Development GIT revision: v3.5.3-2966-g3546a49 GIT Date:
2015-03-12 10:43:22 -0500
[1]PETSC ERROR: darcy on a arch-darwin-c-debug named Johns-MacBook-Air.local by
jposunz Sat Mar 14 08:07:25 2015
[1]PETSC ERROR: Configure options --download-fblaslapack --useThreads=0
--download-triangle --download-netcdf --download-exodusii --download-hdf5
--download-ptscotch --download-chaco
[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for
trouble shooting.
[0]PETSC ERROR: Petsc Development GIT revision: v3.5.3-2966-g3546a49 GIT Date:
2015-03-12 10:43:22 -0500
[0]PETSC ERROR: [1]PETSC ERROR: #1 PetscSectionCreateGlobalSection() line 1010
in /Users/jposunz/projects/src/petsc/src/vec/is/utils/vsectionis.c
[1]PETSC ERROR: #2 DMGetDefaultGlobalSection() line 3269 in
/Users/jposunz/projects/src/petsc/src/dm/interface/dm.c
[1]PETSC ERROR: #3 DMCreateGlobalVector_Section_Private() line 13 in
/Users/jposunz/projects/src/petsc/src/dm/interface/dmi.c
[1]PETSC ERROR: #4 DMCreateGlobalVector_Plex() line 1170 in
/Users/jposunz/projects/src/petsc/src/dm/impls/plex/plexcreate.c
[1]PETSC ERROR: #5 DMCreateGlobalVector() line 698 in
/Users/jposunz/projects/src/petsc/src/dm/interface/dm.c
darcy on a arch-darwin-c-debug named Johns-MacBook-Air.local by jposunz Sat Mar
14 08:07:25 2015
[0]PETSC ERROR: Configure options --download-fblaslapack --useThreads=0
--download-triangle --download-netcdf --download-exodusii --download-hdf5
--download-ptscotch --download-chaco
[0]PETSC ERROR: #1 PetscSectionCreateGlobalSection() line 1010 in
/Users/jposunz/projects/src/petsc/src/vec/is/utils/vsectionis.c
[0]PETSC ERROR: #2 DMGetDefaultGlobalSection() line 3269 in
/Users/jposunz/projects/src/petsc/src/dm/interface/dm.c
[0]PETSC ERROR: #3 DMCreateGlobalVector_Section_Private() line 13 in
/Users/jposunz/projects/src/petsc/src/dm/interface/dmi.c
[0]PETSC ERROR: #4 DMCreateGlobalVector_Plex() line 1170 in
/Users/jposunz/projects/src/petsc/src/dm/impls/plex/plexcreate.c
[0]PETSC ERROR: #5 DMCreateGlobalVector() line 698 in
/Users/jposunz/projects/src/petsc/src/dm/interface/dm.c
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD
with errorcode 62.
--
Dr John O'Sullivan
Lecturer
Department of Engineering Science
University of Auckland, New Zealand
email: jp.osullivan at
auckland.ac.nz<https://lists.mcs.anl.gov/mailman/listinfo/petsc-dev>
tel: +64 (0)9 923 85353
________________________________
From: Matthew Knepley [[email protected]]
Sent: Friday, 13 March 2015 11:57 p.m.
To: John O'Sullivan
Cc: [email protected]
Subject: Re: More on FV overlap cells and Fortran
On Fri, Mar 13, 2015 at 4:56 AM, John O'Sullivan
<[email protected]<mailto:[email protected]>> wrote:
Hi Matt,
We're getting there with our parallel Fortran FV code. But here's another
question about the best way to do things. Another simpleTest2 code is attached
to demonstrate the question and below is a copy of the relevant part:
<mailto:[email protected]>! We worked out its important not to write to the
parts of arrays that correspond to overlap cells.
! Following ex11 it would be done something like this using C:
!
! ierr = DMPlexPointGlobalRef(dm,c,x,&xc);CHKERRQ(ierr);
! if (xc) {ierr =
(*mod->solution)(mod,0.0,cg->centroid,xc,mod->solutionctx);CHKERRQ(ierr);}
!
! And according to the documentation on DMPlexPointGlobalRef xc would be
returned as null for
! the overlap blocks that don't belong to the processor
!
! We can achieve the same using the ghost labels on the overlap cells but is
this a good
! idea? We'd prefer to follow the standard approach ie in ex11 but I don't
think there's a
! clean way to do this in fortran as we can't pass pointers to structures...
! Could it be done with DMPlexPointGlobalRef? If so, any ideas?
I can do two things:
a) Make a Fortran version of DMPlexPointGlobalRef(), which returns an F90
array of size dof
or
b) Make a Fortran wrapper for DMPlexGetGlobalOffset_Internal(), which returns
start/end, and
start < 0 if its off-process
Tell me what you think is better. Also, you can see here that we are
experimenting with different
interfaces. Jed likes getting a pointer back. I like getting offsets back.
Thanks,
Matt
do c = start_cell, end_interior_cell-1
! ??? call DMPlexPointGlobalRef(dm, c, localx, someref)???
call DMLabelGetValue(label, c, ghost, ierr); CHKERRQ(ierr)
if (ghost < 0) then
call PetscSectionGetOffset(solution_section, c, cell_offset, ierr);
CHKERRQ(ierr)
cell_offset = cell_offset + 1
localx(cell_offset) = 100.0
end if
end do
Cheers!
John
--
Dr John O'Sullivan
Lecturer
Department of Engineering Science
University of Auckland, New Zealand
email: jp.osullivan at
auckland.ac.nz<https://lists.mcs.anl.gov/mailman/listinfo/petsc-dev>
tel: +64 (0)9 923 85353
________________________________
From: Matthew Knepley [mailto:[email protected]<mailto:[email protected]>]
Sent: Friday, 13 March 2015 4:44 a.m.
To: John O'Sullivan
Cc: [email protected]<mailto:[email protected]>
Subject: Re: Simple Test example not working in parallel for
DMPlex/FV/overlap/ghost cells...
On Thu, Mar 12, 2015 at 4:19 AM, John O'Sullivan
<[email protected]<mailto:[email protected]>> wrote:
Hi Matt,
Attached is a simple test program where I'm loading the simpleblock-100.exo and
trying to set up a grid with closed boundaries on all the outer faces.
Just so I understand what you want. You do not want any ghost cells made around
the outer boundary. What you have will do that.
We'd like to do it this way so we can use the same sort of architecture as in
PetscFVM to skip ghost faces when calculating fluxes (like you suggested in
your response yesterday)
Note that now, it will also mark the outer boundary faces as ghosts because
they have no partner cell.
It works fine on a single processor but when we run it on 2 processors there's
an indexing error when trying to create a matrix. There's obviously something
wrong with the way we're setting up the dm but I don't know what it is? Or
perrhaps we're not allowed to use DMPlexConstructGhostCells in this way? Also I
was surprised by the values given for end_interior_cell on each processor as it
seems to include the overlap cells which is not what I expected?
This is a bug in my latest preallocation push. Thanks for finding it. I pushed
a fix for this, and for many Fortran things
to next. I am including my modified source so that everything is deallocated
correctly (run with -malloc_test).
It seems to work for me now. Let me know if you have problems.
Thanks,
Matt
One last thing, the FORTRAN interface for DMPlexCreateLabel was missing so I
added it into zplexlabel.c which works fine but I'm not sure if this was the
right way to do it. My version is attached.
The full output from the program for two processors is below.
Cheers
John
(ps Is there a way to make DMView output the Labels information for all
processors?)
$ mpirun -n 2 simpleTest2
DM Object:Parallel Mesh 2 MPI processes
type: plex
Parallel Mesh in 3 dimensions:
0-cells: 12 16
1-cells: 20 28
2-cells: 11 16
3-cells: 2 3
Labels:
ClosedBoundaries: 0 strata of sizes ()
Face Sets: 3 strata of sizes (2, 2, 5)
Cell Sets: 1 strata of sizes (2)
depth: 4 strata of sizes (12, 20, 11, 2)
DM Object: 2 MPI processes
type: plex
DM_0x7f91c1d27ff0_0 in 3 dimensions:
0-cells: 12 16
1-cells: 20 28
2-cells: 11 16
3-cells: 2 (0) 3 (0)
Labels:
ghost: 2 strata of sizes (1, 10)
vtk: 1 strata of sizes (1)
Cell Sets: 1 strata of sizes (2)
Face Sets: 3 strata of sizes (2, 2, 5)
ClosedBoundaries: 0 strata of sizes ()
0 3 3 19 35
depth: 4 strata of sizes (12, 20, 11, 2)
0 2 2 14 25
[1]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[1]PETSC ERROR: Argument out of range
[1]PETSC ERROR: Section point -1 should be in [1, 3)
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: Argument out of range
[0]PETSC ERROR: Section point -3 should be in [0, 1)
[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for
trouble shooting.
[0]PETSC ERROR: Petsc Development GIT revision: v3.5.3-2945-g6900bc9 GIT Date:
2015-03-10 18:15:26 -0500
[0]PETSC ERROR: simpleTest2 on a arch-darwin-c-debug named
Johns-MacBook-Air.local by jposunz Thu Mar 12 22:01:26 2015
[0]PETSC ERROR: Configure options --download-fblaslapack --useThreads=0
--download-triangle --download-netcdf --download-exodusii --download-hdf5
--download-ptscotch --download-chaco
[0]PETSC ERROR: #1 PetscSectionGetDof() line 499 in
/Users/jposunz/projects/src/petsc/src/vec/is/utils/vsectionis.c
[0]PETSC ERROR: #2 DMPlexUpdateAllocation_Static() line 609 in
/Users/jposunz/projects/src/petsc/src/dm/impls/plex/plexpreallocate.c
[0]PETSC ERROR: #3 DMPlexPreallocateOperator() line 763 in
/Users/jposunz/projects/src/petsc/src/dm/impls/plex/plexpreallocate.c
[0]PETSC ERROR: #4 DMCreateMatrix_Plex() line 746 in
/Users/jposunz/projects/src/petsc/src/dm/impls/plex/plex.c
[0]PETSC ERROR: [1]PETSC ERROR: See
http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
[1]PETSC ERROR: Petsc Development GIT revision: v3.5.3-2945-g6900bc9 GIT Date:
2015-03-10 18:15:26 -0500
[1]PETSC ERROR: simpleTest2 on a arch-darwin-c-debug named
Johns-MacBook-Air.local by jposunz Thu Mar 12 22:01:26 2015
#5 DMCreateMatrix() line 958 in
/Users/jposunz/projects/src/petsc/src/dm/interface/dm.c
[1]PETSC ERROR: Configure options --download-fblaslapack --useThreads=0
--download-triangle --download-netcdf --download-exodusii --download-hdf5
--download-ptscotch --download-chaco
[1]PETSC ERROR: #1 PetscSectionGetDof() line 499 in
/Users/jposunz/projects/src/petsc/src/vec/is/utils/vsectionis.c
[1]PETSC ERROR: #2 DMPlexUpdateAllocation_Static() line 609 in
/Users/jposunz/projects/src/petsc/src/dm/impls/plex/plexpreallocate.c
[1]PETSC ERROR: #3 DMPlexPreallocateOperator() line 763 in
/Users/jposunz/projects/src/petsc/src/dm/impls/plex/plexpreallocate.c
[1]PETSC ERROR: #4 DMCreateMatrix_Plex() line 746 in
/Users/jposunz/projects/src/petsc/src/dm/impls/plex/plex.c
[1]PETSC ERROR: #5 DMCreateMatrix() line 958 in
/Users/jposunz/projects/src/petsc/src/dm/interface/dm.c
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD
with errorcode 63.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
--
Dr John O'Sullivan
Lecturer
Department of Engineering Science
University of Auckland, New Zealand
email: jp.osullivan at
auckland.ac.nz<https://lists.mcs.anl.gov/mailman/listinfo/petsc-dev>
tel: +64 (0)9 923 85353
________________________________
From: Matthew Knepley [[email protected]<mailto:[email protected]>]
Sent: Thursday, 12 March 2015 3:06 a.m.
To: John O'Sullivan
Cc: [email protected]<mailto:[email protected]>
Subject: Re: [petsc-dev] DMPlex, Finite Volume, overlap and ghost cells...
On Wed, Mar 11, 2015 at 3:34 AM, John O'Sullivan
<[email protected]<mailto:[email protected]>> wrote:
Hi all,
I've managed to get myself very confused about how to use DMPlex correctly for
a distributed Finite Volume grid...
My understanding was that along partition boundaries the ghost cells are used
store cell information from neighbouring partitions so that the fluxes can be
calculated.
Though debugging through ex11 it seems like overlap is set equal to 1?
I'm solving a simple pressure-diffusion equation on a 1D column (from an exo
grid) which works fine on a single processor but not in parallel. I'm certainly
not setting things up right or labeling correctly...
Could someone please explain the most appropriate way to set up and label the
DM, whether the overlap should be 0 or 1 and whether ghost cells should be
placed on internal partition boundaries.
Yes, for FV the partition overlap should be 1, as it is in ex11. This means
that when the partition happens, we will
put a layer of cells on the other side of partition boundaries,
When DMPlexConstructGhostCells() is called, it will put ghost cells on the
other side of the true boundary. Both
kinds of cells will be separated from interior cells by the
DMPlexGetHybridBounds(&cMax), where cMax is the
first ghost cell.
Now you still need a way to get rid of faces between ghost cells (which only
occur in cells across a partition boundary).
To do this, you use the "ghost" label we make during partitioning:
ierr = DMPlexGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr);
ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr);
if (ghost >= 0) continue;
What exactly is going wrong?
Matt
Thanks!
John
--
Dr John O'Sullivan
Lecturer
Department of Engineering Science
University of Auckland, New Zealand
email: jp.osullivan at
auckland.ac.nz<https://lists.mcs.anl.gov/mailman/listinfo/petsc-dev>
tel: +64 (0)9 923 85353
--
What most experimenters take for granted before they begin their experiments is
infinitely more interesting than any results to which their experiments lead.
-- Norbert Wiener
--
What most experimenters take for granted before they begin their experiments is
infinitely more interesting than any results to which their experiments lead.
-- Norbert Wiener
--
What most experimenters take for granted before they begin their experiments is
infinitely more interesting than any results to which their experiments lead.
-- Norbert Wiener
--
What most experimenters take for granted before they begin their experiments is
infinitely more interesting than any results to which their experiments lead.
-- Norbert Wiener
